The agricultural sector is a source of greenhouse gas emissions that directly affect the global problem of climate change and contribute approximately 11% in total greenhouse gas emissions in the world and in Croatia too. Irregular and irresponsible agricultural practices, such as excessive tillage and improper fertilization often lead to soil carbon loss and increased carbon dioxide emissions to the atmosphere. This field study provides results how agricultural practices affect carbon dioxide emissions from soil, carbon sequestration and soil quality during the cultivation of winter wheat. The field experiment was conducted in a temperate continental climate on distric Stagnosol. Four investigated treatments were: organic fertilization, mineral fertilization, control treatment and black fallow. The lowest carbon dioxide emission was recorded on bare soil and the highest on organic fertilization treatment. The application of manure, mineral fertilizers and calcification rendered significant effect on some soil chemical characteristics and daily carbon dioxide flux.